[UPDATED August 2015 with updates in italic . – Paul]
Bowel diseases are characterized by chronic infection of the gut lining (and sometimes immune cells), wounded and inflamed gut tissue, and autoimmune attacks on the gut.
Malnutrition contributes to bowel disease by impairing immunity, impairing gut motility, and slowing intestinal healing.
Conversely, bowel diseases impair nutrient absorption along with the rest of digestion, exacerbating malnutrition. To avoid a vicious spiral, bowel disease patients should be especially attentive to their nutritional needs.
The first step toward good nutrition is to eat the Perfect Health Diet, including all of our supplemental foods. For gut health, egg yolks are especially important. Also important are extracellular matrix components from bones and joints; vegetables, herbs, and spices; and healthy fats (which trigger bile production, bile being beneficial for the gut). See our Recommended Supplements page for more on the supplemental foods.
We no longer recommend taking a multivitamin. For various reasons multivitamin formulas are incomplete:
- Some nutrients, such as magnesium and vitamin C, are too bulky to fit in a single pill.
- Some, such as vitamin D and iodine, have no “one size fits all” dose that manufacturers can safely include. They therefore include a low dose that is safe for all, meaning that most receive an insufficiency.
- Others, like melatonin, may be unnecessary for the general population but are likely to benefit bowel disease patients.
Here, then, are a few supplements that bowel disease patients may find to be helpful additions to their multivitamin.
Vitamin D3 and Partners
Vitamin D has been called the “antibiotic vitamin”  because it triggers the body’s production of natural antibiotic compounds.
Vitamin D is needed for the production of the antimicrobial peptides cathelicidin and beta-defensin 2, which are produced mainly in immune cells and in epithelial cells lining the gut. [2, 3] These antimicrobial peptides normally saturate the mucosal barrier, where they kill most bacteria, enveloped viruses, fungi, and protozoa.
Evidence has accumulated that deficiencies in antimicrobial peptides are causal factors in bowel diseases:
- In Crohn’s disease, a deficiency of antimicrobial peptides allows pathogens to invade. [4, 5, 6]
- Reduced expression of intestinal defensins predicts diarrhea two months in advance. 
- When antimicrobial peptides are induced therapeutically, intestinal infections are relieved. 
- Mice with no vitamin D function due to knockout of the vitamin D receptor experience bacterial overgrowth of the intestine, and even mild injury to the colon results in the death of the mouse. 
There is increasing awareness that vitamin D is needed for defense against infections generally. 
Vitamin D has other benefits besides strengthening immunity. It also suppresses autoimmunity. For instance, there is evidence for an inverse relationship between vitamin D levels and auto-antibody levels . Some autoimmune patients have experienced a disappearance of auto-antibodies upon supplementation with vitamin D. 
Since bowel diseases are the result of infections and autoimmunity, normalization of vitamin D levels is probably extremely helpful.
Vitamin D is also associated with reduced risk of colorectal cancer.  Bowel disease patients are at elevated risk for colorectal cancer.
Sunshine should be sought regularly, and supplements added to bring serum 25-hydroxyvitamin D levels to at least 40 ng/ml. In addition, vitamin D should be accompanied by supplementation of two key partners:
- Vitamin K2 is needed for proper vitamin D function. Most inflammatory bowel disease patients are severely deficient in vitamin K2.  A good daily supplement should include 100 mcg of the MK-7 form, perhaps combined with some synthetic MK-4 and plant-derived vitamin K1.
- Magnesium is needed for proper vitamin D function and many people are deficient. 200 mg/day magnesium citrate (which is better absorbed than magnesium oxide) is appropriate.
Melatonin is a crucial hormone which is evolutionarily conserved across all nearly all animals, indicating that it is essential to health. Most know that it is produced in the pineal gland of the brain during sleep, but it is less well known that it is abundantly produced by the gut. Much of the body’s melatonin gathers in the gut, where melatonin concentrations are 100-fold greater than in blood and 400-fold greater than in the pineal gland. 
In the gut melatonin reduces inflammation, stimulates immune function, fosters tissue repair and helps regenerate the epithelium.  Melatonin also has antimicrobial effects. 
Clinical trials have found that melatonin can be beneficial in treating bowel conditions. [17, 18, 19] Melatonin seems to be especially effective at reducing abdominal pain. [20, 21]
To maximize night-time melatonin levels, it is best to sleep in a totally darkened room; avoid eating food at night; and avoid exercising at night. Melatonin can also be supplemented. Supplemental melatonin should be taken immediately before bed. Time-release tablets are best, otherwise fluctuating melatonin levels may cause waking in the middle of the night. If early waking does occur, reduce the dose.
Thyroid and Immune Minerals: Selenium and Iodine
Selenium and iodine are critical for thyroid and immune function. Adequate thyroid hormone and a well-functioning immune system, in turn, are essential for gut health.
The thyroid hormone T4 is 65% iodine by weight, and the active thyroid hormone T3 is 59% iodine by weight. Selenium-containing deiodinase enzymes are required to convert inactive thyroid hormone to its active form. Either iodine or selenium deficiency can cause hypothyroidism, or a deficiency of thyroid hormone.
Gut problems, especially constipation, are among the primary symptoms of hypothyroidism. Thyroid hormone is important for proper wound healing – and therefore for recovery from bowel disease.
Selenium and iodine are also essential for immune function. Iodine along with the enzyme myeloperoxidase is needed to produce respiratory bursts – the burst of reactive oxygen species (ROS) that white blood cells use to kill pathogens. Selenium is necessary both to strip iodine from thyroid hormone in the white blood cells, and to maintain (via the enzyme glutathione peroxidase) the function of the antioxidant glutathione which protects both white blood cells and gut cells from ROS. Deficiency of either selenium or iodine leads to an immediate reduction in the killing activity of white blood cells.
Iodine was widely prescribed for infectious diseases in the 19th century. The Nobel laureate Dr. Albert Szent Györgyi, the discoverer of vitamin C, recounted this anecdote:
When I was a medical student, iodine in the form of KI was the universal medicine. Nobody knew what it did, but it did something and did something good. We students used to sum up the situation in this little rhyme:
If ye don’t know where, what, and why
Prescribe ye then K and I. 
Doses as large as 1 gram potassium iodide, containing 770 mg of iodine, were given. In practice, however, it’s highly desirable to start with a low dose of iodine, around 1 mg/day, and allow the thyroid to adapt before gradually increasing the dose.
The great danger of high doses of iodine is that it will make autoimmune attacks, as well as attacks on pathogens, more powerful. Therefore large supplemental doses of iodine should be taken only after grains and legumes have been eliminated from the diet for at least 3 months. Bowel disease patients should also be tested for the presence of thyroid auto-antibodies before beginning high-dose iodine.
- Myeloperoxidase requires iron (heme), and unfortunately anemia due to iron deficiency is common in bowel disease patients, especially among menstruating women.  A good way to judge the need for iron is to measure blood ferritin levels, which should be 50 ng/ml or higher.
If auto-antibodies are present, then hypothyroidism cannot be repaired by iodine supplementation. Yet thyroid hormone is necessary for gut healing. In such cases, prescription thyroid hormone should be taken.
Hypothyroidism is widely undiagnosed, because the “normal” range of thyroid stimulating hormone (TSH) is far too wide. TSH levels over 1.5 mIU/L may indicate a subclinical hypothyroidism that is sufficient to measurably raise mortality.  Anyone with a TSH over 1.5 mIU/L and a basal body temperature below 98 F should consider obtaining prescription thyroid hormone to test whether it helps relieves hypothyroidism-associated symptoms such as constipation and improves general health. Generally, a good dose of thyroid hormone will eliminate symptoms of hypothyroidism and reduce TSH to 2.0 or so – still elevated, to stimulate thyroid healing.
Antioxidants and Bile Supports: Vitamin C, Glutathione, N-Acetylcysteine, Taurine, Glycine
Since the main immune defense (and autoimmune) mechanisms in the gut involve around ROS-producing respiratory bursts, the gut of any bowel disease patient is a ROS-rich environment.
It is therefore desirable to maximize the ability of both gut and immune cells to protect themselves against ROS with native antioxidants.
Foremost among the native antioxidants is glutathione, the primary immune and gut antioxidant. Glutathione may be supplemented directly, or its levels may be raised by supplementing with vitamin C and N-acetylcysteine.
Vitamin C has other important functions: it is needed for wound healing and to maintain the collagen-based extracellular matrix which backs the gut and gives it integrity. One of the symptoms of scurvy (extreme vitamin C deficiency) is bleeding from the mucus membranes, including the gut lining.
A Japanese study found that vitamin C was highly protective against ulcerative colitis, reducing incidence by 55%. 
In rats, glutathione deficiency leads to elevated infection-induced bowel inflammation.  Glycine (the most abundant amino acid in extracellular matrix) and taurine both support glutathione synthesis.
- Zinc and copper are both required for the function of another antioxidant, zinc-copper superoxide dismutase. We recommend supplementing dietary intake with another 15 mg zinc and 2 mg copper. This can be achieved by taking a daily multivitamin plus eating occasional beef or lamb liver.
- Magnesium is needed for glutathione synthesis. As noted before, 200 mg/day magnesium citrate is a highly desirable supplement for bowel disease patients.
Magnesium and copper deficiencies contribute to necrotizing enterocolitis , and probably worsen all bowel diseases.
Bile is an important aid to gut health, in part because it helps to clear the small intestine of bacteria. Bile needs vitamin C for its manufacture and needs to be conjugated with glycine or taurine. Glycine can be obtained from food as extracellular matrix material, or as a powder which you can sprinkle on food. Taurine is an excellent supplement for patients with gut disorders.
Although not a complete list of the vitamins and minerals which may be helpful to bowel disease patients, these are among the most important – and most often overlooked:
- Vitamin D3 sufficient to raise serum 25-hydroxyvitamin D above 40 ng/ml.
- Vitamin K2, at least 100 mcg/day.
- Magnesium citrate or bis-glycinate, 200 mg/day.
- Melatonin, if needed for deep restful sleep.
- Selenium, 200 mcg/week.
- Iodine, 225 mcg/day.
- Thyroid hormone sufficient to bring TSH below 2.0.
- Vitamin C, 1 g/day.
- Glutathione, 500 mg/day, preferably in the reduced form, taken between meals on an empty stomach with a full glass of water (since it is destroyed by stomach acid).
- N-acetylcysteine, 500 mg/day.
- Iron, zinc, and copper sufficient to relieve deficiencies.
- Taurine, 1 g/day.
- Glycine (if insufficient extracellular matrix is eaten), up to 5 g/day.
Other posts in this series:
- Bowel Disorders, Part I: About Gut Disease July 14, 2010
- Bowel Disease, Part II: Healing the Gut By Eliminating Food Toxins m July 19, 2010
- Bowel Disease, Part IV: Restoring Healthful Gut Flora July 27, 2010
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